@Override
public List<Integer> getLeaves() {
int externalNodeCount = tree.getExternalNodeCount();
List<Integer> leaves = new ArrayList<Integer>(externalNodeCount);
for (int i = 0; i < externalNodeCount; ++i) leaves.add(tree.getExternalNode(i).getNumber());
return leaves;
}
public double[] getSummaryStatistic(Tree tree) {
double externalLength = 0.0;
double internalLength = 0.0;
int externalNodeCount = tree.getExternalNodeCount();
for (int i = 0; i < externalNodeCount; i++) {
NodeRef node = tree.getExternalNode(i);
externalLength += tree.getBranchLength(node);
}
int internalNodeCount = tree.getInternalNodeCount();
for (int i = 0; i < internalNodeCount; i++) {
NodeRef node = tree.getInternalNode(i);
if (!tree.isRoot(node)) {
internalLength += tree.getBranchLength(node);
}
}
return new double[] {internalLength + externalLength};
}